Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002361.1 Kokia drynarioides strain JFW-HI SEQ_114432, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111071
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:573 original size:12 final size:12
Alignment explanation
Indices: 558--608 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
548 GAAAGAGAGC
558 GAGAGGGAGGGA
1 GAGAGGGAGGGA
*
570 GAGAGGCAGGGA
1 GAGAGGGAGGGA
*
582 GAGAGAGA-GG-
1 GAGAGGGAGGGA
*
592 GAGAGCGAGGGA
1 GAGAGGGAGGGA
604 GAGAG
1 GAGAG
609 ATTAGATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.21
11 4 0.12
12 22 0.67
ACGTcount: A:0.35, C:0.04, G:0.61, T:0.00
Consensus pattern (12 bp):
GAGAGGGAGGGA
Found at i:580 original size:16 final size:16
Alignment explanation
Indices: 561--608 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
551 AGAGAGCGAG
561 AGGGAGGGAGAGAGGC
1 AGGGAGGGAGAGAGGC
* *
577 AGGGAGAGAGAGAGGG
1 AGGGAGGGAGAGAGGC
593 AGAGCGAGGGAGAGAG
1 AG-G-GAGGGAGAGAG
609 ATTAGATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 16 0.59
17 1 0.04
18 10 0.37
ACGTcount: A:0.35, C:0.04, G:0.60, T:0.00
Consensus pattern (16 bp):
AGGGAGGGAGAGAGGC
Found at i:602 original size:22 final size:24
Alignment explanation
Indices: 558--609 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
548 GAAAGAGAGC
* *
558 GAGAGGGAGGGAGAGAGGCAGGGA
1 GAGAGAGAGGGAGAGACGCAGGGA
582 GAGAGAGAGGGAGAG-CG-AGGGA
1 GAGAGAGAGGGAGAGACGCAGGGA
604 GAGAGA
1 GAGAGA
610 TTAGATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 11 0.42
23 1 0.04
24 14 0.54
ACGTcount: A:0.37, C:0.04, G:0.60, T:0.00
Consensus pattern (24 bp):
GAGAGAGAGGGAGAGACGCAGGGA
Found at i:2224 original size:24 final size:23
Alignment explanation
Indices: 2164--2228 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
2154 AGGTGTTCTA
*
2164 TTATATATTTTTATATTTTCTTT
1 TTATATATTTTTATAATTTCTTT
* * *
2187 TATTTAAATATTTATAATTTCATTT
1 T-TATATATTTTTATAATTTC-TTT
2212 TTATATATTTTTA-AATT
1 TTATATATTTTTATAATT
2229 AAACCATTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.15
24 24 0.73
25 4 0.12
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATATATTTTTATAATTTCTTT
Found at i:2959 original size:26 final size:26
Alignment explanation
Indices: 2923--2975 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2913 AGTTTATGTA
2923 TTCTAATCTTCCCTTCCCTCAAACCC
1 TTCTAATCTTCCCTTCCCTCAAACCC
2949 TTCTAATCTTCCCTTCCCTCAAACCC
1 TTCTAATCTTCCCTTCCCTCAAACCC
2975 T
1 T
2976 AGTCTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.36
Consensus pattern (26 bp):
TTCTAATCTTCCCTTCCCTCAAACCC
Found at i:3584 original size:41 final size:41
Alignment explanation
Indices: 3519--3599 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
3509 GAAGGTAAAG
* *
3519 GGTTAATATATATGGAGAGTGAGAGATTAGATGAAGATTAT
1 GGTTAATATAAATGGAGAGGGAGAGATTAGATGAAGATTAT
*
3560 GGTTAATATAAATGTAGAGGGAGAGATTAGATGAAGATTA
1 GGTTAATATAAATGGAGAGGGAGAGATTAGATGAAGATTA
3600 GATAAACCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (41 bp):
GGTTAATATAAATGGAGAGGGAGAGATTAGATGAAGATTAT
Found at i:5642 original size:52 final size:50
Alignment explanation
Indices: 5549--5716 Score: 153
Period size: 52 Copynumber: 3.4 Consensus size: 50
5539 TTTTAGAACT
* * * *
5549 TATTTATCTAAATTGTTTTGTTTAGATATGGTGTTTTATATAAAAATAAA
1 TATTTATTTAAATTGTTTTGTTCAGATATAGTGTTTGATATAAAAATAAA
* * *
5599 TATTTATTTAAATTGTTTTTTGTTCGGATCTAGTGTTTGATATAAATATAAA
1 TATTTATTTAAATTG--TTTTGTTCAGATATAGTGTTTGATATAAAAATAAA
* * * * * * *
5651 TATTTATTT--ATT-TTTTGTTCAAATTTGGTATTTTACATAAATATAAA
1 TATTTATTTAAATTGTTTTGTTCAGATATAGTGTTTGATATAAAAATAAA
* *
5698 TATTTATTTATATTTTTTT
1 TATTTATTTAAATTGTTTT
5717 TAGATCTTGT
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
47 37 0.37
49 3 0.03
50 21 0.21
52 38 0.38
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (50 bp):
TATTTATTTAAATTGTTTTGTTCAGATATAGTGTTTGATATAAAAATAAA
Found at i:6424 original size:82 final size:82
Alignment explanation
Indices: 6174--6768 Score: 568
Period size: 82 Copynumber: 7.4 Consensus size: 82
6164 TAAAAATTAA
* * * * *
6174 AATTGAATAAATCTGTTTTGGGATTTATTCCCGTCGTTCATCAGATTTTATTCTATTGTGATTTT
1 AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTTT
* *
6239 GTTT-CAAAAAACGATT
66 GTTTCCAAACAAGGATT
* * * * * * *
6255 AAATT-AATAAATT-TGCTTCGGGATTTATTCTCGCCGTTTTAA-AAATTTTATTCTATTTTGA-
1 -AATTGAAT-AATTCTGTTTCGAGATTTATTCCCGTCG-TTCAACAGATTTTATTCTATTATGAT
6316 TTT-TTTCCAAACAAGGATT
63 TTTGTTTCCAAACAAGGATT
* * * * *
6335 AATTGAATAATTCTATTTCGAGATTTATTCCCGCCATTCAACAGATTCTCTTCTATTATGATTTT
1 AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTTT
6400 GTTTCCAAACAAGGATT
66 GTTTCCAAACAAGGATT
* * * * *
6417 AATTGAATAATTCTGTTTCGAGATTTATTCACGCCGTTCAACTGATTTT-TTCCTATTTTGAATT
1 AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATT-CTATTATGATTT
*
6481 TGTTTCCAAACAACGATT
65 TGTTTCCAAACAAGGATT
* ** * *
6499 AATTGAATAATTCTGTTTTG-GAATTTATTCCTATCGTACAACAGGTTTTATTCTATTATGATTT
1 AATTGAATAATTCTGTTTCGAG-ATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTT
* *
6563 TCTTTCCAAACAAGAATT
65 TGTTTCCAAACAAGGATT
* ** * * * *
6581 AATAGAATAATTCTACTTCGAGATTTATTTCTGTTGTTCAATAGATTTTATTCTATTATGATTTT
1 AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTTT
* *
6646 GTTTGCAAACAAGAATT
66 GTTTCCAAACAAGGATT
* * *** * * * *
6663 AATTGAATAATTCTTTTTTGAGATTTATTATTGTCATTCAATAGA----ATT-GATTTTGATTTT
1 AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTTT
*
6723 GTTTCCAAACAAGAATT
66 GTTTCCAAACAAGGATT
* * *
6740 AATTAAATAATTTTGTTTCAAGATTTATT
1 AATTGAATAATTCTGTTTCGAGATTTATT
6769 TTTGCCGTTC
Statistics
Matches: 431, Mismatches: 70, Indels: 29
0.81 0.13 0.05
Matches are distributed among these distances:
77 50 0.12
78 3 0.01
79 15 0.03
80 49 0.11
81 45 0.10
82 266 0.62
83 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (82 bp):
AATTGAATAATTCTGTTTCGAGATTTATTCCCGTCGTTCAACAGATTTTATTCTATTATGATTTT
GTTTCCAAACAAGGATT
Found at i:9480 original size:15 final size:15
Alignment explanation
Indices: 9460--9503 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
9450 GAGGTGTTCT
9460 ATTTTATATTTTTAA
1 ATTTTATATTTTTAA
*
9475 ATTTTATTTTATTTAA
1 ATTTTATATT-TTTAA
9491 ATATTTATGATTT
1 AT-TTTAT-ATTT
9504 CATTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 7 0.29
17 6 0.25
18 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
ATTTTATATTTTTAA
Found at i:11030 original size:70 final size:69
Alignment explanation
Indices: 10918--11056 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 69
10908 TGCACCATTC
*
10918 TTGCAGTTGGGTTTTTTTTGATAAAAAACCAAAAGCAAAGGGTTAGTATATATGGAGGGAGGGAG
1 TTGCAGCTGGGTTTTTTTTGATAAAAAACCAAAAGCAAAGGGTTAGTATATATGGAGGGAGGGAG
10983 AGAG
66 AGAG
10987 TTGCAGCTGGGTTTTTTTTTGATAAAAAACCAAAAGCAAAGGGTTAGTATATATGGAGGGAGGGA
1 TTGCAGCTGGG-TTTTTTTTGATAAAAAACCAAAAGCAAAGGGTTAGTATATATGGAGGGAGGGA
11052 GAGAG
65 GAGAG
11057 ATGGGGGAAG
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 10 0.15
70 58 0.85
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.27
Consensus pattern (69 bp):
TTGCAGCTGGGTTTTTTTTGATAAAAAACCAAAAGCAAAGGGTTAGTATATATGGAGGGAGGGAG
AGAG
Found at i:13359 original size:164 final size:159
Alignment explanation
Indices: 13088--13471 Score: 423
Period size: 164 Copynumber: 2.4 Consensus size: 159
13078 GTCATTGCGC
* * * * ** *
13088 CCAAACAAGGATTAATTGAATAATTCTGTTTCAGGATTTATTCCTACCAATCAAAAAATTTTATT
1 CCAAACAAGAATTAATAGAATAATTCTATTTCAGGATTTATTCCTATCGTTCAACAAATTTTATT
* * * * *
13153 CTATTTTAATTTTGATTCCAAGCAATGATTAATTGAATAATTCTATTTTGAA-ATTTATTCCAAT
66 CTACTCTAATTTTGATTCCAAACAATGATTAATTGAATAATTCT-GTTTCAAGATTTATTCCAAT
* *
13217 CGTACAACAGATTTTATTGTATTATGATTTTGTTT
130 CATACAACAGA----ATTG-ATTATGATTATGTTT
** * *
13252 CCAAACAAGAATTAATAGAATAATTCTATTTTGGGATTTATTCCCATTGTTCAACAAATTTTATT
1 CCAAACAAGAATTAATAGAATAATTCTATTTCAGGATTTATTCCTATCGTTCAACAAATTTTATT
* * **
13317 CTACTCTGATTTTGTTTCCAAACAA-GAATTAATTGAATAATTCTGTTTCAAGATTTATTCCTGT
66 CTACTCTAATTTTGATTCCAAACAATG-ATTAATTGAATAATTCTGTTTCAAGATTTATTCCAAT
* * *
13381 CATTCAATAGAATTGATTTTGATTATGTTT
130 CATACAACAGAATTGATTATGATTATGTTT
* *
13411 CCAAACAAGAATTAATTA-AATAATTCCATTTCAGTATTTATTCCTATCGTTCAACATAATT
1 CCAAACAAGAATTAA-TAGAATAATTCTATTTCAGGATTTATTCCTATCGTTCAACA-AATT
13472 GATTTTGATT
Statistics
Matches: 185, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
159 60 0.32
160 10 0.05
163 6 0.03
164 109 0.59
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (159 bp):
CCAAACAAGAATTAATAGAATAATTCTATTTCAGGATTTATTCCTATCGTTCAACAAATTTTATT
CTACTCTAATTTTGATTCCAAACAATGATTAATTGAATAATTCTGTTTCAAGATTTATTCCAATC
ATACAACAGAATTGATTATGATTATGTTT
Found at i:13387 original size:82 final size:81
Alignment explanation
Indices: 13088--13471 Score: 370
Period size: 82 Copynumber: 4.7 Consensus size: 81
13078 GTCATTGCGC
* * * * ** *
13088 CCAAACAAGGATTAATTGAATAATTCTGTTTCAGGATTTATTCCTACCAATCAAAAAATTTTATT
1 CCAAACAAGAATTAATTGAATAATTCTATTTCAAGATTTATTCCTATCGTTCAACAAATTTTATT
* *
13153 CTATTTTAATTTTGATT
66 CTA-TTTGATTTTGTTT
* * * * *
13170 CCAAGCAATG-ATTAATTGAATAATTCTATTTTGAA-ATTTATTCCAATCGTACAACAGATTTTA
1 CCAAACAA-GAATTAATTGAATAATTCTA-TTTCAAGATTTATTCCTATCGTTCAACAAATTTTA
*
13233 TTGTATTATGATTTTGTTT
64 TTCTATT-TGATTTTGTTT
* *** * *
13252 CCAAACAAGAATTAATAGAATAATTCTATTTTGGGATTTATTCCCATTGTTCAACAAATTTTATT
1 CCAAACAAGAATTAATTGAATAATTCTATTTCAAGATTTATTCCTATCGTTCAACAAATTTTATT
*
13317 CTACTCTGATTTTGTTT
66 CTA-TTTGATTTTGTTT
* * * * *
13334 CCAAACAAGAATTAATTGAATAATTCTGTTTCAAGATTTATTCCTGTCATTCAATAGAA-TTGA-
1 CCAAACAAGAATTAATTGAATAATTCTATTTCAAGATTTATTCCTATCGTTCAACA-AATTTTAT
*
13397 --T-TTTGATTATGTTT
65 TCTATTTGATTTTGTTT
* *
13411 CCAAACAAGAATTAATTAAATAATTCCATTTC-AGTATTTATTCCTATCGTTCAACATAATT
1 CCAAACAAGAATTAATTGAATAATTCTATTTCAAG-ATTTATTCCTATCGTTCAACA-AATT
13472 GATTTTGATT
Statistics
Matches: 248, Mismatches: 45, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
76 2 0.01
77 60 0.24
78 1 0.00
79 1 0.00
81 6 0.02
82 170 0.69
83 8 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (81 bp):
CCAAACAAGAATTAATTGAATAATTCTATTTCAAGATTTATTCCTATCGTTCAACAAATTTTATT
CTATTTGATTTTGTTT
Found at i:13433 original size:77 final size:77
Alignment explanation
Indices: 13232--13481 Score: 236
Period size: 77 Copynumber: 3.2 Consensus size: 77
13222 AACAGATTTT
* * * ** *
13232 ATTGTATTATGATTTTGTTTCCAAACAAGAATTAA-TAGAATAATTCTATTTTGGGATTTATTCC
1 ATTG-ATTTTGATTATGTTTCCAAACAAGAATTAATTA-AATAATTCCATTTCAGTATTTATTCC
* **
13296 CATTGTTCAACA-A
64 TATCATTCAACAGA
* * * **
13309 ATTTTATTCTACTCTGATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTGTTTCAAG-ATTT
1 A-TTGA-T-T--T-TGATTATGTTTCCAAACAAGAATTAATTAAATAATTCCATTTC-AGTATTT
* *
13373 ATTCCTGTCATTCAATAGA
59 ATTCCTATCATTCAACAGA
13392 ATTGATTTTGATTATGTTTCCAAACAAGAATTAATTAAATAATTCCATTTCAGTATTTATTCCTA
1 ATTGATTTTGATTATGTTTCCAAACAAGAATTAATTAAATAATTCCATTTCAGTATTTATTCCTA
* *
13457 TCGTTCAACATA
66 TCATTCAACAGA
13469 ATTGATTTTGATT
1 ATTGATTTTGATT
13482 TTTTTCAAAA
Statistics
Matches: 143, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
76 2 0.01
77 73 0.51
78 4 0.03
79 1 0.01
80 1 0.01
81 1 0.01
82 57 0.40
83 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (77 bp):
ATTGATTTTGATTATGTTTCCAAACAAGAATTAATTAAATAATTCCATTTCAGTATTTATTCCTA
TCATTCAACAGA
Found at i:16072 original size:50 final size:50
Alignment explanation
Indices: 16012--16179 Score: 185
Period size: 50 Copynumber: 3.3 Consensus size: 50
16002 TCAAAACACG
* * * *
16012 TTTATCTAAATTGTTTTATTCAGATCTGGTGTTTTATATAAAAATATATA
1 TTTATTTAAATTGTTTTATTCAGATATGGTGTTTTATATAAATATAAATA
* * *
16062 TTTATTTAAATGTTTTTTTGTTCAAATATGGTGTTTTATATAAATATAAATA
1 TTTATTTAAA--TTGTTTTATTCAGATATGGTGTTTTATATAAATATAAATA
* * * * *
16114 TTTA-TTAATTTTTTTTTCTTCAGATATGATGTTTTACATAAATATAAATA
1 TTTATTTAA-ATTGTTTTATTCAGATATGGTGTTTTATATAAATATAAATA
*
16164 TTTATTTATATTGTTT
1 TTTATTTAAATTGTTT
16180 GTTCAAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
50 54 0.55
51 7 0.07
52 38 0.38
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (50 bp):
TTTATTTAAATTGTTTTATTCAGATATGGTGTTTTATATAAATATAAATA
Found at i:16094 original size:52 final size:52
Alignment explanation
Indices: 16038--16171 Score: 191
Period size: 50 Copynumber: 2.6 Consensus size: 52
16028 TATTCAGATC
* * *
16038 TGGTGTTTTATATAAAAATATATATTTATTTAAATGTTTTTTTGTTCAAATA
1 TGGTGTTTTATATAAATATAAATATTTATTTAAATGTTTTTTTCTTCAAATA
* *
16090 TGGTGTTTTATATAAATATAAATATTTA-TT-AATTTTTTTTTCTTCAGATA
1 TGGTGTTTTATATAAATATAAATATTTATTTAAATGTTTTTTTCTTCAAATA
* *
16140 TGATGTTTTACATAAATATAAATATTTATTTA
1 TGGTGTTTTATATAAATATAAATATTTATTTA
16172 TATTGTTTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 43 0.59
51 4 0.05
52 26 0.36
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (52 bp):
TGGTGTTTTATATAAATATAAATATTTATTTAAATGTTTTTTTCTTCAAATA
Found at i:17666 original size:40 final size:40
Alignment explanation
Indices: 17622--17731 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
17612 GATAGAGAAA
*
17622 GCCGCAAAAGGTAAAGCATTAGCGGCGTTTTTCCATAAAC
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCATAAAC
* * *
17662 GCCGCAATAGGTAAAGCAATAGCAGAGTTTTTCCATAAAC
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCATAAAC
*
17702 GCCACAAAAGGTAAAGCAATAGCGGCGTTT
1 GCCGCAAAAGGTAAAGCAATAGCGGCGTTT
17732 ATAAAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (40 bp):
GCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCATAAAC
Found at i:17848 original size:41 final size:41
Alignment explanation
Indices: 17738--17886 Score: 127
Period size: 41 Copynumber: 3.6 Consensus size: 41
17728 GTTTATAAAA
* * * * *
17738 AAAACGCCGCTAAAGGTTAGAGCATTAGCAGCGCTTATGGG
1 AAAATGCCACTAAAGATCAGAGCATTAGCAGCGCTTATGAG
* * * * * * *
17779 AAAATGCCACTAATGCTCTGACCTTTAGCGGCGTTTATGAG
1 AAAATGCCACTAAAGATCAGAGCATTAGCAGCGCTTATGAG
* * *
17820 AAAATGCTACTAAAGATCAGAGCATTAGCAGCACTTATGGG
1 AAAATGCCACTAAAGATCAGAGCATTAGCAGCGCTTATGAG
** * *
17861 AAAGCGCCGCTAAAGGTCAGAGCATT
1 AAAATGCCACTAAAGATCAGAGCATT
17887 CTAAATGTCG
Statistics
Matches: 82, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAATGCCACTAAAGATCAGAGCATTAGCAGCGCTTATGAG
Found at i:17900 original size:17 final size:17
Alignment explanation
Indices: 17870--17903 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17860 GAAAGCGCCG
17870 CTAAAGGTCAGAGCATT
1 CTAAAGGTCAGAGCATT
* *
17887 CTAAATGTCGGAGCATT
1 CTAAAGGTCAGAGCATT
17904 AGCGGCGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
CTAAAGGTCAGAGCATT
Found at i:17970 original size:40 final size:41
Alignment explanation
Indices: 17887--18056 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 41
17877 TCAGAGCATT
* * **
17887 CTAAATGTCGGAGCATTAGCGGCGCTTATGGGAAAGCGTCG
1 CTAAAGGTCGGAGCATTAGCGGCGCTTATGAGAAAGCACCG
*
17928 CTAAAGGTCGGAGCATTAGTGG-GCTTATGAGAAAGCACCG
1 CTAAAGGTCGGAGCATTAGCGGCGCTTATGAGAAAGCACCG
** * * * * *
17968 CTAAAGGTTAGAGCATTAGCGGCACTTTCTCATAAA-CGCCG
1 CTAAAGGTCGGAGCATTAGCGGCGC-TTATGAGAAAGCACCG
** * ** * *
18009 CTAAAGGTCATAGTATTAGCGATGTTTATG-GAAAGCGCCG
1 CTAAAGGTCGGAGCATTAGCGGCGCTTATGAGAAAGCACCG
18049 CTAAAGGT
1 CTAAAGGT
18057 TAGGCAATAG
Statistics
Matches: 103, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
39 3 0.03
40 50 0.49
41 43 0.42
42 7 0.07
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAAAGGTCGGAGCATTAGCGGCGCTTATGAGAAAGCACCG
Found at i:21801 original size:42 final size:43
Alignment explanation
Indices: 21631--21804 Score: 235
Period size: 42 Copynumber: 4.1 Consensus size: 43
21621 ATGTTAATGA
* *
21631 TAGCGGCGTTTGTGAGAAAAGCATCGCTGAAGACCATGTTCTT
1 TAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGACCATGTTCTT
* * *
21674 CAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTT
1 TAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGACCATGTTCTT
* * *
21717 CAGCGGCGTTTGTG-GGAAAGCACCGGTAAAGACCATGTTCTT
1 TAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGACCATGTTCTT
* * *
21759 TAGCGGTGTTTGTG-GGAAAGCACTGCTAAAGACCATGTTCTT
1 TAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGACCATGTTCTT
21801 TAGC
1 TAGC
21805 AGCATTTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 67 0.57
43 51 0.43
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGACCATGTTCTT
Found at i:25983 original size:23 final size:23
Alignment explanation
Indices: 25957--26003 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
25947 TGCTGACTAA
25957 ACCTTCTAGAAGCTACTGACTGG
1 ACCTTCTAGAAGCTACTGACTGG
*
25980 ACCTTCTAGAAGCTATTGACTGG
1 ACCTTCTAGAAGCTACTGACTGG
26003 A
1 A
26004 TGCCACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (23 bp):
ACCTTCTAGAAGCTACTGACTGG
Found at i:26807 original size:14 final size:13
Alignment explanation
Indices: 26789--26833 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
26779 TTTTTCGAAC
*
26789 CTTTTTCTTTTTT
1 CTTTTTTTTTTTT
*
26802 CTTTTTTTTCTATT
1 CTTTTTTTT-TTTT
26816 CTTTTTTTTTCTTT
1 CTTTTTTTTT-TTT
26830 CTTT
1 CTTT
26834 ATTCGAACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:26836 original size:21 final size:21
Alignment explanation
Indices: 26789--26837 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
26779 TTTTTCGAAC
26789 CTTT-TTCTTTTTTCTTTTTT
1 CTTTATTCTTTTTTCTTTTTT
26809 -TTCTATTCTTTTTT-TTTCTTT
1 CTT-TATTCTTTTTTCTTT-TTT
26830 CTTTATTC
1 CTTTATTC
26838 GAACTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.08
20 4 0.16
21 17 0.68
22 2 0.08
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (21 bp):
CTTTATTCTTTTTTCTTTTTT
Found at i:26851 original size:53 final size:50
Alignment explanation
Indices: 26764--26865 Score: 116
Period size: 53 Copynumber: 2.0 Consensus size: 50
26754 CTCCTTTTAT
* ** *
26764 TTCTCTTTTTTTTTTTTTTTCGAACCTTTTTCTTTTTTCTTTTTTTTCTA
1 TTCTCTTTTTTTTTTTTTTTCGAACCTCTTTCTTTGCTCTCTTTTTTCTA
*
26814 TTCTTTTTTTTTCTTTCTTTATTCGAA-CTCCTTTCTTTGCTCTCTTTTTTCT
1 TTCTCTTTTTTT-TTT-TTT-TTCGAACCT-CTTTCTTTGCTCTCTTTTTTCT
26866 TATATTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 11 0.26
51 3 0.07
52 5 0.12
53 24 0.56
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.72
Consensus pattern (50 bp):
TTCTCTTTTTTTTTTTTTTTCGAACCTCTTTCTTTGCTCTCTTTTTTCTA
Found at i:31749 original size:23 final size:23
Alignment explanation
Indices: 31714--31763 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
31704 TGTCCATCCT
*
31714 TGCTGACTAGACCTTCTAGAAGC
1 TGCTAACTAGACCTTCTAGAAGC
*
31737 TGCTAACTGGACCTTCTAGAAGC
1 TGCTAACTAGACCTTCTAGAAGC
31760 TGCT
1 TGCT
31764 GAATGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (23 bp):
TGCTAACTAGACCTTCTAGAAGC
Found at i:31770 original size:23 final size:23
Alignment explanation
Indices: 31714--31770 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
31704 TGTCCATCCT
* *
31714 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGAATGGACCTTCTAGAAGC
31737 TGCT-AACTGGACCTTCTAGAAGC
1 TGCTGAA-TGGACCTTCTAGAAGC
31760 TGCTGAATGGA
1 TGCTGAATGGA
31771 TTCTAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 27 0.90
24 2 0.07
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (23 bp):
TGCTGAATGGACCTTCTAGAAGC
Found at i:33046 original size:21 final size:23
Alignment explanation
Indices: 33021--33065 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
33011 ATTTTTTATC
*
33021 TAATTTC-GTTGTAA-CAATTTA
1 TAATTTCAGTAGTAATCAATTTA
33042 TAATTTCAGTAGTAATCAATTTA
1 TAATTTCAGTAGTAATCAATTTA
33065 T
1 T
33066 CAACATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
TAATTTCAGTAGTAATCAATTTA
Found at i:34621 original size:28 final size:28
Alignment explanation
Indices: 34581--34644 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
34571 GAGAGTGAAG
*
34581 GAGAGACAGAGAGAGG-GAGGGATGGAGGGA
1 GAGAGAAAGAGAG-GGAGAGGGA--GAGGGA
*
34611 GAGAGAAAGAGGGGGAGAGGGAGAGGGA
1 GAGAGAAAGAGAGGGAGAGGGAGAGGGA
34639 GAGAGA
1 GAGAGA
34645 TTAGATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 12 0.39
29 2 0.06
30 17 0.55
ACGTcount: A:0.39, C:0.02, G:0.58, T:0.02
Consensus pattern (28 bp):
GAGAGAAAGAGAGGGAGAGGGAGAGGGA
Found at i:34628 original size:14 final size:14
Alignment explanation
Indices: 34605--34644 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34595 GGGAGGGATG
34605 GAGGGAGAGAGAAA
1 GAGGGAGAGAGAAA
* **
34619 GAGGGGGAGAGGGA
1 GAGGGAGAGAGAAA
34633 GAGGGAGAGAGA
1 GAGGGAGAGAGA
34645 TTAGATAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (14 bp):
GAGGGAGAGAGAAA
Found at i:35627 original size:186 final size:186
Alignment explanation
Indices: 35310--35651 Score: 431
Period size: 186 Copynumber: 1.8 Consensus size: 186
35300 TCGTTGTAAC
* * *
35310 GATTTATAATTTCAGTAGTAATCAGTTTATCGACATACATGTGTTCTGTTATATATGTTTTTGAA
1 GATTTATAATTTCAATAGTAATCAGTTTATCGACATACATGTGTTCTATTATATACGTTTTTGAA
* * * * * * * *
35375 TTTTTTTATGTATTTATTGATGTGCATATTCCTTATCTCATACTTTACAATGAGTTTGTCAACTT
66 TTTTTTTATGCATTCATTGATGTACATATTACTTATCACATACATTACAACGAGTTTATCAACTT
35440 ACACGTACTCTATTTTATATTCTTGAATTAAATTTTTCCTTCCATTTCAATGCAAA
131 ACACGTACTCTATTTTATATTCTTGAATTAAATTTTTCCTTCCATTTCAATGCAAA
* * *
35496 GATTTATAATTTCAATTGTAGT-AGTTTATCGACTTACATGTGTTCTATTATAT-CG-TTTTGAA
1 GATTTATAATTTCAATAGTAATCAGTTTATCGACATACATGTGTTCTATTATATACGTTTTTGAA
* * ** *
35558 TTTAATTGTTTTGCATTCATTGTTGTACATATTAAC-TATCACATACATTGGAACGGGTTTATCA
66 TTT--TT-TTATGCATTCATTGATGTACATATT-ACTTATCACATACATTACAACGAGTTTATCA
* *
35622 ACTTACACGTGCTTTATTTTATATTCTTGA
127 ACTTACACGTACTCTATTTTATATTCTTGA
35652 CCTATTTTTT
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
183 10 0.08
184 1 0.01
185 31 0.24
186 88 0.67
187 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.47
Consensus pattern (186 bp):
GATTTATAATTTCAATAGTAATCAGTTTATCGACATACATGTGTTCTATTATATACGTTTTTGAA
TTTTTTTATGCATTCATTGATGTACATATTACTTATCACATACATTACAACGAGTTTATCAACTT
ACACGTACTCTATTTTATATTCTTGAATTAAATTTTTCCTTCCATTTCAATGCAAA
Found at i:37922 original size:41 final size:41
Alignment explanation
Indices: 37835--37924 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
37825 AAAGGGTTAA
* * * * * *
37835 CATATATGGAGAGTGAGAGATTAGATGAAGATTATGGTTAG
1 CATATATTGAGAGGGAGAGATTAGATAAAGATTATGATAAC
*
37876 TATATATTGAGAGGGAGAGATTAGATAAAGATTA-GATAAAC
1 CATATATTGAGAGGGAGAGATTAGATAAAGATTATGAT-AAC
37917 CATATATT
1 CATATATT
37925 ACACTTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.05
41 38 0.95
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (41 bp):
CATATATTGAGAGGGAGAGATTAGATAAAGATTATGATAAC
Found at i:45095 original size:12 final size:12
Alignment explanation
Indices: 45078--45102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45068 GCCAACACTT
45078 TAATAGCATTCA
1 TAATAGCATTCA
45090 TAATAGCATTCA
1 TAATAGCATTCA
45102 T
1 T
45103 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:48114 original size:36 final size:36
Alignment explanation
Indices: 48074--48145 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
48064 TCATGTATCG
48074 GAAGAAGTACAGAGTAGGGGAGAGGTTGGTTACTGA
1 GAAGAAGTACAGAGTAGGGGAGAGGTTGGTTACTGA
*
48110 GAAGAAGTACAGAGTGGGGGAGAGGTTGGTTACTGA
1 GAAGAAGTACAGAGTAGGGGAGAGGTTGGTTACTGA
48146 CTTACATTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.43, T:0.19
Consensus pattern (36 bp):
GAAGAAGTACAGAGTAGGGGAGAGGTTGGTTACTGA
Found at i:48297 original size:21 final size:21
Alignment explanation
Indices: 48256--48297 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
48246 TTAGTATTGG
*
48256 TAGAAGCATGACATGTTTCGA
1 TAGAAGCATGACATGTATCGA
*
48277 TAGAAGTCAT-ACTTGTATCGA
1 TAGAAG-CATGACATGTATCGA
48298 CAGTATTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.31
Consensus pattern (21 bp):
TAGAAGCATGACATGTATCGA
Found at i:49920 original size:2 final size:2
Alignment explanation
Indices: 49893--49943 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
49883 AATATATATG
* * * * *
49893 GA GA GT GA GA GT GA AA GA GA GG GA GA GA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
49935 GA GA GA GA G
1 GA GA GA GA G
49944 GGAGGGAGAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04
Consensus pattern (2 bp):
GA
Found at i:65407 original size:22 final size:23
Alignment explanation
Indices: 65366--65408 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
65356 TAGTCTTAGA
* *
65366 TTAACTTAATTAAGCTTAATTAT
1 TTAACTTAATTAAACATAATTAT
65389 TTAAC-TAATTAAACATAATT
1 TTAACTTAATTAAACATAATT
65409 TCTAAGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAACTTAATTAAACATAATTAT
Found at i:66351 original size:17 final size:17
Alignment explanation
Indices: 66316--66357 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
66306 GAAAAAAGTA
*
66316 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
66334 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
66351 GTTAAAG
1 GTTAAAG
66358 GTAAAAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:66357 original size:24 final size:24
Alignment explanation
Indices: 66330--66377 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
66320 CAAGAATATG
* *
66330 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTAAAAGAAGATGAAAGGTT
*
66354 AAAGGTAAAAGGAGATGAAAGGTT
1 AAAGGTAAAAGAAGATGAAAGGTT
66378 GAACATCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (24 bp):
AAAGGTAAAAGAAGATGAAAGGTT
Found at i:69073 original size:13 final size:13
Alignment explanation
Indices: 69055--69080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69045 CATCTCAAGG
69055 AGGTAAAATATTA
1 AGGTAAAATATTA
69068 AGGTAAAATATTA
1 AGGTAAAATATTA
69081 GCTCTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
AGGTAAAATATTA
Found at i:72162 original size:40 final size:39
Alignment explanation
Indices: 72109--72238 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 39
72099 TTGAGTTTGT
* *
72109 AACAGAGTCGTGAGATCAGCTCGCACATATCAGAATCATG
1 AACA-AGTTGTGAGATCAGCTCACACATATCAGAATCATG
72149 AACTAAGTTGTGAGATCAGCTCACACATATCAGAATCATG
1 AAC-AAGTTGTGAGATCAGCTCACACATATCAGAATCATG
* * *
72189 AACAGAGTCT-TGAGATTAGCTCACACATATCAAAAACATG
1 AACA-AGT-TGTGAGATCAGCTCACACATATCAGAATCATG
72229 AACAAAGTTG
1 AAC-AAGTTG
72239 GCAATAGGTC
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.03
40 75 0.94
41 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (39 bp):
AACAAGTTGTGAGATCAGCTCACACATATCAGAATCATG
Found at i:72668 original size:18 final size:18
Alignment explanation
Indices: 72634--72669 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
72624 AAATTCTTGT
* *
72634 TAAAATAAAATACAGTAA
1 TAAAATAAAACAAAGTAA
72652 TAAAATAAAACAAAGTAA
1 TAAAATAAAACAAAGTAA
72670 AGTCCAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (18 bp):
TAAAATAAAACAAAGTAA
Found at i:77007 original size:17 final size:17
Alignment explanation
Indices: 76985--77035 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
76975 TTCGTTGAGA
76985 GTTCGTGTGAAGAACTT
1 GTTCGTGTGAAGAACTT
77002 GTTCGT-TG-AG-A---
1 GTTCGTGTGAAGAACTT
77013 GTTCGTGTGAAGAACTT
1 GTTCGTGTGAAGAACTT
77030 GTTCGT
1 GTTCGT
77036 TGAGAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 6 0.21
12 2 0.07
13 2 0.07
14 2 0.07
15 2 0.07
16 2 0.07
17 12 0.43
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (17 bp):
GTTCGTGTGAAGAACTT
Found at i:77007 original size:28 final size:28
Alignment explanation
Indices: 76967--77040 Score: 148
Period size: 28 Copynumber: 2.6 Consensus size: 28
76957 GAAGAGGTGG
76967 AGAACTTGTTCGTTGAGAGTTCGTGTGA
1 AGAACTTGTTCGTTGAGAGTTCGTGTGA
76995 AGAACTTGTTCGTTGAGAGTTCGTGTGA
1 AGAACTTGTTCGTTGAGAGTTCGTGTGA
77023 AGAACTTGTTCGTTGAGA
1 AGAACTTGTTCGTTGAGA
77041 ATTTGTCCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.35
Consensus pattern (28 bp):
AGAACTTGTTCGTTGAGAGTTCGTGTGA
Found at i:78215 original size:7 final size:7
Alignment explanation
Indices: 78203--78232 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
78193 ACGCTCATTA
78203 TATCACT
1 TATCACT
78210 TATCACT
1 TATCACT
78217 TATCACT
1 TATCACT
78224 TATCACT
1 TATCACT
78231 TA
1 TA
78233 AAGTCGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (7 bp):
TATCACT
Found at i:82044 original size:15 final size:15
Alignment explanation
Indices: 82024--82053 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82014 AAATTTGGCT
82024 TTTTGTGACATTTTC
1 TTTTGTGACATTTTC
*
82039 TTTTGTGACGTTTTC
1 TTTTGTGACATTTTC
82054 GAAAATGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTTGTGACATTTTC
Found at i:82519 original size:22 final size:21
Alignment explanation
Indices: 82477--82525 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
82467 AATCAATTTC
82477 TGTGACATTTTTTGAATTTTTT
1 TGTGACA-TTTTTGAATTTTTT
*
82499 TGTGACA-TTTTGAGA-TATTT
1 TGTGACATTTTTGA-ATTTTTT
82519 TGTGACA
1 TGTGACA
82526 ATTTCCTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.22, C:0.06, G:0.18, T:0.53
Consensus pattern (21 bp):
TGTGACATTTTTGAATTTTTT
Found at i:84402 original size:28 final size:28
Alignment explanation
Indices: 84362--84444 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
84352 AAAACACCAG
84362 AAACTCTAGAAAGGTAAGCCTTTGTGAC
1 AAACTCTAGAAAGGTAAGCCTTTGTGAC
* * * * *
84390 AAAC-CTTTGAAAGGAAATTCCTCTGTGGC
1 AAACTC-TAGAAAGGTAA-GCCTTTGTGAC
84419 AAACTCTAGAAAGGTAAGCCTTTGTG
1 AAACTCTAGAAAGGTAAGCCTTTGTG
84445 GCAATCTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.02
28 20 0.47
29 21 0.49
30 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (28 bp):
AAACTCTAGAAAGGTAAGCCTTTGTGAC
Found at i:95657 original size:12 final size:12
Alignment explanation
Indices: 95642--95676 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
95632 TGCTCACCAT
*
95642 CATGATCATGAC
1 CATGATCATCAC
95654 CATGATCATCAC
1 CATGATCATCAC
*
95666 CATCATCATCA
1 CATGATCATCA
95677 TGATAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.31, G:0.09, T:0.26
Consensus pattern (12 bp):
CATGATCATCAC
Done.